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AP Bio First Semester Review Geo

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Emma DeJarnette

on 24 October 2015

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Transcript of AP Bio First Semester Review Geo

GENETIC MATERIAL
Both DNA and RNA are made up of a sugar-phosphate backbone with a nitrogenous base attached. Held together by hydrogen bonds.
DNA has bases G, C, A, T and the sugar is deoxy-ribose. Dbl stranded, antiparallel directionally.
RNA has bases G, C, A, U, and the sugar is ribose. Single stranded.
Both have either a 5' end or a 3' end because of the alternating sugar-phosphate.
Genetics
Cell Cycle
By replication of somatic cells through mitosis, the body grows, and repairs.

By dividing somatic cells into gametes in meiosis, the body produces a gamete with 23 chromosomes, and if it combines with another gamete, will form a zygote. The zygote will grow into an embryo and eventually into a child/independent body.

More Basic Genetics
Mono-hybrid cross: parents are both heterozygous for a trait.
AP Biology Review First Semester
Hey Coach C. Wassup.

Bases in DNA
Mitosis
The cell cycle begins with the 3 stages of Interphase:
G1: A cell grows. If it doesn't pass the G1 checkpoint, it enters G0, and becomes a non-dividing cell like muscle/nerve.
S Phase: Grows more and replicates it's chromosomes. Has Checkpoint.
G2 Phase: Grows even more, prepares for M stage. Checkpoint is passed by the presence of MPF.
Purines bond with pyrimidines.
M Phase (Mitosis) is the duplication of the nucleus. Has 4 stages:
Prophase: Chromatin coils into chromatin and the nuclear membrane dissolves.
Metaphase: Chromosomes are arranged in the middle of the cell, and spindle fibers attach to the kinetochore.
Anaphase: Spindle fibers are destroyed by kinetochore and chromosomes pulled to opposite poles.
Telophase: Nuclei begin to form and the beginnings of cleavage of a cell plate forms.
M phase is followed by cytokinesis, which is the division of the cytoplasm and organelles into two functioning daughter cells.
Mitosis: More in Depth

MPF, maturation promoting factor, is the complex of cyclin and cyclin-dependent kinases (Cdks) which allows for the cell to pass the G2 checkpoint. CdKs are always present and when cyclin becomes concentrated in the cell, the resulting MPFs rise. Therefore, the mitotic phase is dependent on the presence of cyclin.

Each of the two sister chromatids of a replicated chromosome has a kinetochore, a structure of proteins at the centromere. Spindle micro tubules attach here and the kinetochore disassembles the fibers, moving to opposite poles = Anaphase.
Meiosis undergoes 2 divisions: Meiosis 1 and Meiosis 2. Same stages in each division: prophase, metaphase, anaphase, telophase+cytokinesis.
Binary Fission in prokaryotes is not mitosis. The circular chromosome replicates and is pulled to opposite ends of the cell.
Chromosome Theory of Inheritance: Genes have specific loci along chromosomes and it is the individual chromosomes that undergo segregation and independent assortment.
Law of Segregation: Two alleles coding for a specific trait on different chromosomes separate into different gametes.
Law of Ind. Assort.: Each pair of alleles separates independently.
Di-hybrid cross: Parents are heterozygous for two traits.


Degrees of Dominance
Incomplete Dominance: Hybrids have a phenotype somewhere between those of the parents.
Co-dominanace: Both phenotypes are expressed and expressed alleles are distinct.
Even More Genetics~
Pleiotropy: a property of alleles causing more than one phenotype.


Epistasis: gene at one locus alters phenotypic expression of a gene at a second locus.
Polygenic Inheritance: Two or more genes affect a trait. Ex: skin.

Wild Type: the phenotype most commonly observed in natural populations. Expressed by x+
Mutant Phenotypes: alternatives to wild types. Expressed by x.

Sex-Linked: On X or Y chromosome. If X-linked, males will always express. On X in humans.
Barr body: the other inactive X on each cell of a female condenses into compact object.

Linked Genes: 2 or more genes located on the same chromosome that are usually inherited together in genetic crosses.
When crossing over occurs between homologous chromosomes during prophase, linked genes can be separated. The closer a gene is to another gene, the smaller the recombination frequency.
Results in recombinants, which have genotypes different from either of the parents.



Have you ever asked yourself wtf polyploidy and aneuploidy is? Well this circle is for you.
Polyploidy: When organisms have more than 2 complete chromosome sets.
Triploidy (3n), Tetraploidy (4n)
common in plants
Aneuploidy: When the zygote has an abnormal number of chromosomes.
Monosomy: Missing chromosome=2n-1
Trisomy: One extra chromosome=2n+1
ex: down syndrome

ALL OF THE ABOVE IS CAUSED BY NON-DISJUNCTION: homologous chromosomes/sister chromatids don't move apart properly during meiosis

Disclaimer: The 'F' in the WTF above refers to 'Flagella'.
Hershey and Chase proved DNA/RNA is the genetic material of cells.
DNA Replication
Results in 4 sexy gametes (haploids). Occurs in the gonads. woooo sex.
So..... you may be wondering how this 'cell' that replicates came to be..... (of course you are)
Th
e Conditions of Early Earth made life possible:
1. Synthesis of small organic molecules like amino acids and nucleotides
2. Macromolecules like proteins, nucleic acids
3. Packaging into a Protobiont
4. Origin of self-replicating molecules

Protobionts- the precursor to living cells
-resulted in amino acids/ other organic compounds from inorganic compounds

Miller-Urey experiment

-simulated Early Earth conditions
Therefore, it's thought that Early Earth oceans may have been a giant 'primordial soup' where organic compounds arose.

These compounds rose from carbon dioxide, methane, nitrogen and its oxides, ammonia, hydrogen, and hydrogen sulfide.

The energy for this synthesis may have come from lightning and intense UV radiation.






RNA which plays an integral role in protein synthesis also carries out enzyme-like functions.

RNA catalysts- Ribozymes

RNA may have carried the information of protobionts (precursors to living cells)

Protobionts = structures bound by lipid membrane (called liposome) that could swell/shrink
The Geologic Record provides evidence for the idea that all organisms come from a common ancestor of life (UCA!!!!!
Universal Common Ancestor
)

The age of the rocks where a fossil is found, the rate of decay of isotopes including carbon-14, the relationships within phylogenetic trees, and the mathematical calculations that take into account information from chemical properties and/or geographical data.


Endosymbiosis- idea that mitochondria and chloroplasts began to live inside other cells (got engulfed)
Geologic Record
When we look at these fossils, we see the phenotype (expressed characteristic) of

Homeotic genes- regulatory genes determining where structures in organism should be located (spatially and placement)

Hox genes- positional information
Many phyla of living animals occured in the Cambrian period-- known as the Cambrian Explosion!!!

Continental Drift- continents move away from each other (No Mo' Pangaea :-( )

Several mass extinction events due to environmental conditions

Adaptive Radiation occured as a result--
organisms formed many new species whose adaptations allowed them to fill different niches.
KEY POINT:

EVOLUTION IS NOT GOAL ORIENTED

Mutations (imperfect DNA Replication) = primary source of genetic variation.
Whether mutation is detrimental, beneficial or neutral depends on environmental context.

Key Point: Individuals don’t evolve, but the population evolves over time based on the accumulation of beneficial traits within an environment

Darwin

Natural Selection/ Descent w/. Modification
-occurs due to environmental interactions with individuals in a population

- results in differential reproductive success and heritable variability
- results in populations adapting to their environment
-Not goal oriented, purely by chance

NATURAL SELECTION
Cuvier
- catastrophism
Lamarck
- inherit acquired traits, use and disuse of traits
Malthus
- overproduction of organisms takes place
Hutton
- gradualism
Linnaeus
- classification system
Wallace
- natural selection with adaptations






Sexual Selection
Mutations can be caused by:

-an external factor, such as UV radiation
-errors/ damages in the DNA Repair/Replication mechanisms
In addition to natural selection, chance and random events can influence the evolutionary process (especially for small populations-- genetic drift, a nonselective process, might take place)

Hardy Weinberg Equilibrium- the assumption that a population does not undergo natural selection (?)

Conditions for Hardy-Weinberg equilibrium:

(1) a large population size,
(2) absence of migration, (no genetic flow)
(3) no new mutations,
(4) random mating
(5) absence of selection.

These conditions are seldom met. If all of these were met, however, this would mean no genetic drift.

p= probability of dominant alleles
q= probability of recessive alleles

p + q = 1
p^2 + pq + q^2 = 1 -genotypic frequency.

Genotypic frequency provides the probability of the particular genotype instead of just the probability of certain alleles


Here, p= .5
q= .5


Fossils are dated using radiometric dating (decay of radioactive isotopes) which is expressed by half-life (the time required for 50% of
a parent isotope to decay)
Molecular, morphological and genetic information of existing and extinct organisms add to our understanding of evolution.

Morphological homologies-
features shared by
common ancestry

Vestigial structures-
remnants of functional structures, which can be compared to fossils and provide evidence for evolution

Biochemical and genetic similarities (DNA nucleotide and protein sequences)
provide evidence for evolution and ancestry



Mathematical models and simulations can be used to illustrate and support evolutionary concepts.
• Graphical analyses of allele frequencies in a population
• Analysis of sequence data sets
• Analysis of phylogenetic trees
• Construction of phylogenetic trees based on sequence data


Phylogenetic trees and cladograms can represent traits that are either derived or lost due to evolution.
• Number of heart chambers in animals
• Opposable thumbs
• Absence of legs in some sea mammals

More on Cladograms/ Phylogenetic Trees
- illustrate speciation that has occurred
(in that relatedness of any two groups on the tree is shown by how recently two groups had a common ancestor)

-can be constructed from morphological similarities of living or fossil species, and from DNA and protein sequence similarities,
(by employing computer programs that have sophisticated ways of measuring and representing relatedness among organisms)

-dynamic
(i.e., phylogenetic trees and cladograms are constantly being revised), based on the biological data used, new mathematical and computational ideas, and current and emerging knowledge.


- can show what has been derived/lost from evolution



Therefore, scientific evidence supports.....

-the idea that evolution has occurred in all species.

-the idea that evolution continues to occur.
• Chemical resistance
(mutations for resistance to antibiotics, pesticides, herbicides or chemotherapy drugs occur in the absence of the chemical)
• Emergent diseases
• Observed directional phenotypic change in a population (
Grants’ observations of Darwin’s finches in the Galapagos)
• A eukaryotic example that describes evolution of a structure or process such as heart chambers, limbs, the brain and the immune system

- the idea that all organisms derive from a common ancestor

-the various models (Hershey & Chase, Darwin, etc.)


e.g. molecular building blocks that are common to all life forms, common genetic code.
using info from geographical, geological, physical, chemical and mathematical applications



Living systems have a variety of signal behaviors or cues that
produce changes in the behavior of other organisms and can result in differential reproductive success.
• Herbivory responses
• Territorial marking in mammals
• Coloration in flowers

Animals use visual, audible, tactile, electrical and chemical signals to indicate dominance, find food, establish territory and ensure reproductive success.
• Bee dances
• Birds songs
• Territorial marking in mammals
• Pack behavior in animals
• Herd, flock, and schooling behavior in animals
• Predator warning
• Colony and swarming behavior in insects
• Coloration variation.

Other stuff that maybe affects reproductive success:
Cooperative behavior tends to increase the fitness of the individual and the survival of the population.
• Pack behavior in animals
• Herd, flock and schooling behavior in animals
• Predator warning
• Colony and swarming behavior in insects

Species-specific and environmental catastrophes, geological events, the sudden influx/depletion of abiotic resources or increased human activities affect species distribution and abundance

Population ability to respond to changes in the environment is affected by genetic diversity. Species and populations with little genetic diversity are at risk for extinction.

Genetic diversity allows individuals in a population to respond differently to the same changes in environmental conditions.

• Not all animals in a population stampede.
• Not all individuals in a population in a disease outbreak are equally affected; some may not show symptoms, some may have mild symptoms, or some may be naturally immune and resistant to the disease.

Reduction of genetic variation within a given population can increase the differences between populations of the same species.

A population of organisms has properties that are different from those of the individuals that make up the population. The cooperation and competition between individuals contributes to these different properties.

Genetic information is transmitted from one generation to the next through DNA or RNA.


transduction
(viral transmission of genetic information)-- bacteria
conjugation
(cell-to-cell transfer)
transposition
(movement of DNA segments within and between DNA molecules) (
transposons
- jumping genes)

Genetic information in retroviruses is a special case and has an alternate flow of information: from RNA to DNA, made possible by reverse transcriptase, an enzyme that copies the viral RNA genome into DNA. This DNA integrates into the host genome and becomes transcribed and translated for the assembly of new viral progeny.

Viruses have highly efficient replicative capabilities that allow for rapid evolution and acquisition of new phenotypes. (transmit DNA or RNA when they infect a host cell)



Viruses & DNA (Celeb #1)
Viruses replicate via component assembly model allowing one virus to produce many progeny simultaneously via the lytic cycle.

RNA viruses lack replication error-checking mechanisms, and thus have higher rates of mutation.

Related viruses can combine/recombine information if they infect the same host cell.

Some viruses are able to integrate into the host DNA and establish a latent (lysogenic) infection.
-can result in new properties for the host such as increased pathogenicity in bacteria (e.g. HIV)

Virus replication allows for mutations to occur through usual host pathways.

The horizontal acquisitions of genetic information primarily in prokaryotes via transformation (uptake of naked DNA)


DNA replication is semi-conservative -------------------------------------->
Replication begins at origins of replication. Helicases (enzymes) unwind dbl helix at replication forks. Single-strand binding proteins stabilize unpaired DNA strands, while Topoisomerases relieve the strain of the paired DNA. In order for DNA lpolymerase to catalyze new DNA, it must have a 3' end to build off of. Primase lay down temporary RNA, primer. A different DNA polymerase replaces the primer with DNA after catalyzing DNA occurs. Ligase then comes in and attaches the replacement DNA to the adjacent DNA strand's 3' end.
Elongation of a DNA strand can only occur in the 5'---->3' direction.
Leading/Lagging Strand and OKAZAKI FRAGMENTS
Because DNA polymerase can only travel in the 5'--->3' direction, one polymerase continually duplicates DNA and is nestled in the replication fork, producing the leading strand . However, the other RNA polymerase must 'jump' to the occasional primers, replicate the DNA until it hits another primer, then 'jump' back 2 more primers and replicate to the first primer. (2 steps forward, one step back kinda thing) Makes progress, but is slower then the leading strand polymerase, causing the LAGGING STRAND. The fragments of primers and the a stretch of DNA on the lagging strands are called Okazaki fragments.

It is important to remember that these replication complexes are stationary and DNA moves through them.
This replication occurs bidirectionally!!!! LOOK AT DIAGRAM FOOOOL.
if they're sexy, they get laid. if they arent they dont get laid. boom.

^basically.

Intrasexual- fighting between species to get the girl

Intersexual- the choosing of the mate

Transcription
INITIATION:
RNA polymerase separates 2 strands after bonding to the promoter region.
Associated with most eukaryotic genes are control elements, segments of non-coding DNA which help regulate transcription by binding certain proteins.
Far away control elements are enhancers. DNA folds to allow enhancers with bonded activators to attach to the mediator proteins, allowing the transcription initiation complex to form. If repressors bond to these enhancers, no transciption.
Cells have different types of enhancers to allow expression of particular genes=differential gene expression.
Elongation:
Polymerase moves downstream, unwinds DNA, and elongates RNA transcript.
Rejoins DNA templates after.
Termination:
A sequence, the terminator, signals for release of transcript and polymerase detaches.
In Eukaryotes, the transcription factors are part of the transciption initiation complex that binds to the promoter with the pomerase and initiates transcription. A eukaryotic promoter includes a TATA box commonly.

Transcription: Synthesis of RNA under the direction of DNA:

RNA Processing
Each RNA transcript recieves a 5' cap (GTP cap?) to it's 5' end and a poly-A tail to it's 3' end. These ends protect from degradation of RNA.
RNA splicing cuts out noncoding DNA segments called introns, and then splice together coding segments called exons. A spliceosome does the editing of the RNA strand.
Alternative RNA splicing (exons becoming introns etc.) allowes for multiple proteins to be produced from the same segment of DNA when different regions are classified as exons.

Once above completed in the nucleus, it is mRNA and ready for exportation to ribosome.
Translation: the journey from a lone mRNA to a cosmopolitan protein~~
mRNA is a sequence of codons, 3 nucleotides, which code for a specific amino acid. When it binds to the ribosome, the start codon is located and translation begins from there, with tRNA's matching anticodons to mRNA's codons, and the amino acid's attached to the tRNA bond together and detach from the ribosome and tRNA, forming a growing polypeptide. When stop codon reached, translation stops and polypeptide released.
Aminoacyl-tRNA synthetase binds amino acid and tRNA together.
tRNA travels through A, P and E bonding sites.
The sequences of amino acids interacts with the environment, affecting the primary structure and therefore the secondary, tertiary, and quaternary structure and function.
RIBOSOMES AND POOOOOP :<
Robosomes made up of rRNA. Large and small subunits of rRNA and other proteins join in cytoplasm to form ribosome.
Mutations
primary source of genetic variation
usefulness of mutation dependent on environmental context
Errors in replication, in DNA repair/fixing mechanisms such as nucleases, or radiation/chemicals can all cause mutations
mutation can alter codons and therefore proteins and therefore phenotypic expression of the protein
ex: point mutations
Rapid speciation can occur through polyploidy.
Environmental factors influence many traits both directly and indirectly.
• Height and weight in humans
• Flower color based on soil pH
• Seasonal fur color in arctic animals
• Sex determination in reptiles
• Density of plant hairs as a function of herbivory
• Effect of adding lactose to a Lac + bacterial culture
• Effect of increased UV on melanin production in animals
• Presence of the opposite mating type on pheromones production in yeast and other fungi

A heterozygote may be a more advantageous genotype than a homozygote under particular conditions, since
with two different alleles, the organism has two forms of proteins that may provide functional resilience in
response to environmental stresses.

Ex: Sickle Cell and malaria resistance in heterozygotes

So when evolution like this occurs, reproductive isolation also occurs.
New species arise from reproductive isolation over time, which can involve scales of hundreds of thousands or even millions of years, or speciation can occur rapidly through mechanisms such as polyploidy in plants.

This supports the idea that organisms diverged from a common ancestor and eventually developed into their own species.
-According to Darwin’s theory of natural selection, competition for limited resources results in differential survival. Individuals with more favorable phenotypes are more likely to survive and produce more offspring, thus passing traits to subsequent generations. Evolutionary fitness is measured by reproductive success.



Genetic variation and mutation play roles in natural selection. A diverse gene pool is important for the
survival of a species in a changing environment.
Environments can be more or less stable or fluctuating, and this affects evolutionary rate and direction;
different genetic variations can be selected in each generation.
An adaptation is a genetic variation that is favored by selection and is manifested as a trait that provides an
advantage to an organism in a particular environment.
In addition to natural selection, chance and random events can influence the evolutionary process, especially for small populations.
Phenotypic variations are not directed by the environment but occur through random changes in the DNA and through new gene combinations
Biochemical and genetic similarities, in particular DNA nucleotide and protein sequences, provide evidence
for evolution and ancestry.
Rules of probability can be applied to analyze passage of single gene traits from parent to offspring.

Genes that are adjacent and close to each other on the same chromosome tend to move as a unit!
the probability that they will segregate as a unit is a function of the distance between them (measured in map units)

Segregation and independent assortment of chromosomes
-result in genetic variation
-can be applied to genes that are on different chromosomes.

The pattern of inheritance (monohybrid, dihybrid, sex-linked, and genes linked on the same homologous chromosome) can often be predicted from data that gives the parent genotype/
phenotype and/or the offspring phenotypes/genotypes.

So how do you measure the probability that your offspring will have certain genes that you have?
Differential Survival
Certain human genetic disorders can be attributed to the inheritance of single gene traits or specific chromosomal changes, such as nondisjunction.

• Sickle cell anemia
• Tay-Sachs disease
• Huntington’s disease
• X-linked color blindness
• Trisomy 21/Down syndrome
• Klinefelter’s syndrome

Many ethical, social and medical issues surround human genetic disorders.
• Reproduction issues
• Civic issues such as ownership of genetic information, privacy, historical contexts, etc.

Many traits are the product of multiple genes and/or physiological processes.

Patterns of inheritance of many traits do not follow ratios predicted by Mendel’s laws and can be identified by quantitative analysis, where observed phenotypic ratios statistically differ
from the predicted ratios.

b. Some traits are determined by genes on sex chromosomes.
• Sex-linked genes reside on sex chromosomes (X in humans).
• In mammals and flies, the Y chromosome is very small and carries few genes.
• In mammals and flies, females are XX and males are XY; as such, X-linked recessive traits are always expressed in males.
• Some traits are sex limited, and expression depends on the sex of the individual, such as milk production in female mammals and pattern baldness in males.

Environmental factors influence many traits both directly and indirectly.
• Height and weight in humans
• Flower color based on soil pH
• Seasonal fur color in arctic animals
• Sex determination in reptiles
• Density of plant hairs as a function of herbivory
• Effect of adding lactose to a Lac + bacterial culture
• Effect of increased UV on melanin production in animals
• Presence of the opposite mating type on pheromones production in yeast and other fungi

An organism’s adaptation to the local environment reflects a flexible response of its genome.

Multiple copies of alleles or genes (gene duplication) may provide new phenotypes.

A heterozygote may be a more advantageous genotype than a homozygote under particular conditions, since with two different alleles, the organism has two forms of proteins that may provide functional resilience in response to environmental stresses.

Gene duplication creates a situation in which one copy of the
gene maintains its original function, while the duplicate may
evolve a new function.
• The antifreeze gene in fish

Natural Selection AKA
Gene Expression
Specific gene expressions can be controlled by:
Operon: the operator, promoter, the gene that are controlled.
Operator's: controls access of RNA polymerase to genes. 'Switches' operon on or off.
A repressible Operon can be switched off by a protein called a repressor(AKA regulatory gene) which binds to the operator and prevents binding of RNA polymerase
Corepressors, small molecules that bind to a repressor protein to switch an operon off.
Regulatory Gene's produce repressors.
More Operons
Inducible Operons (ex: lac operon) are usually off but can be actibvated when a specific small molecule, the inducer, inactivated the repressor (regulatory protein).
During metaphase, one chromosome from papa one from mama.
Apoptosis
programmed cell death. By killing cells in certain areas, results in development of fingers and toes and other morphology.

also helps when theres a nastybutt virus and u can be like NU UN GURLLL and suicide for your mates. immune system swag.
mitosis results in 2 genetically identical daughter cells. asexual.
hey laboni wassup gurrrrl
Full transcript